Life Sciences Commons^™

An Antiviral Response Unleashed: Deciphering The Relationship Between Shiftless And Rna Granules During Kshv Infection, David C. Hatfield

Masters Theses

Herpesviruses persist as a parasitic actor among many species. These viral agents can rapidly seize control over host cells by influencing global gene expression. Through a process known as host shutoff, herpesviruses cause a widespread degradation event of host transcripts within the cytoplasm. Specifically, Kaposi Sarcoma associated herpesvirus (KSHV) encodes for an endoribonuclease, termed SOX, that orchestrates this manipulation of gene expression. We and others have discovered certain transcripts that escape this fate; we suggest that this is an active escape, where transcripts have 3’ UTR elements that disallow SOX cleavage. One of the escapees that has been found is …

Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro

Doctoral Dissertations

During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a …

The Impacts Of Environment And Host Evolutionary Relationships On Lemur Microbiota, Rachel B. Burten

Doctoral Dissertations

Recent studies have shown that the mammal microbiome is modified by environmental conditions, and that reduced microbiome functionality is associated with host health issues. Microbiome data in wild and captive primate populations can therefore be used to assess their health as they encounter a variety of environments. Comparative studies of the microbiome can also inform disease ecology, conservation, and captive management strategies tailored to different primate species. Therefore, this study examines how the hair, oral, and gut microbiota of nine wild and captive lemur species are determined by host phylogenetic relationships and host environment. I found that host species identity …

Detection And Control Of Environmentally Transmissible Viruses, Anand R. Soorneedi

Doctoral Dissertations

Viruses, owing to their ubiquitous nature and ability to infect almost every other species, have long been a subject of interest for scientists. Some of the virus species can be very deadly to humans and animals alike and can impose a huge economic and health burden across the world. The recent CoVID-19 pandemic underscores the importance of timely detection for developing effective intervention strategies. Unfortunately, some of the virus species that cause significant health and economic impacts do not have robust and reliable detection methods due to several reasons. In some cases, despite having gold standard methods for detection of …

A Biochemical Approach To Characterize A Divergent Trypanosoma Brucei Mitochondrial Dna Polymerase, Polib, Stephanie B. Delzell

Doctoral Dissertations

Trypanosoma brucei is a single-celled parasitic protist that causes African sleeping sickness in people and nagana in cattle in sub-Saharan Africa. T. brucei and related trypanosomatid parasites contain an unusual catenated mitochondrial genome known as kinetoplast DNA (kDNA) composed of dozens of 23 kb maxicircles and thousands of 1 kb minicircles. The kDNA structure and replication mechanism are divergent from other eukaryotes and essential for parasite survival. POLIB is one of three Family A DNA polymerases that are independently essential to maintain the kDNA network, and has been implicated in minicircle replication. However, the division of labor among the paralogs, …

The Discovery Of A Novel Bacteria From A Large Co-Assembly Of Metagenomes, Matthew Finkelberg

Masters Theses

In the summer of 2022, a co-assembly of metagenome was created using the microbes found at Barres Woods in Harvard Forest. 14 samples were taken, and sample was split into the organic and mineral layer, which totals 28 Bulk MAGs. Within this Co-assembly, 4 different genomes were found which were designated with the phylum of FCPU426. Three of which were considered medium quality and one being assigned high quality. The novel phyla first appeared in NCBI and GTDB databases in June 2018. The name FCPU426 dates to 2010 and was named based on the 16s amplicon sequencing.

The novel phylum …

Climate Change, Giant Viruses And Their Putative Hosts, Sarah K. Tucker

Masters Theses

Viruses hold our attention for the horrific impact they have on human health and welfare. However, viruses are a critical part of our ecosystem and facilitate the cycling of carbon and other important nutrients. The cycle of virus infection, followed by host resistance and the subsequent evolution of new strains enables adaptation to changing hosts and the environment. Giant viruses, some with particle sizes large enough to be visible in light microscopes and their bewildering array of accessory genes, have captivated scientists and the general public since their discovery two decades ago. Giant viruses are part of the Nucleocytoviricota (NCV) …

Enhanced Killing Of Mycobacterium Abscessus By Nanosponge Delivery Of Antimycobacterials, Casey Albano

Masters Theses

The increasing prevalence of bacterial infections has made it necessary to find novel methods of combatting the resistance of bacteria to conventional antibiotics. Mycobacterium abscessus is an increasingly prevalent pathogen that is intrinsically drug resistant, therefore difficult to treat. The use of phytochemicals as a source of alternate antibiotics has been explored, however, the poor solubility of phytochemicals in water makes it difficult to effectively deliver them to bacterial biofilms. In this study, I investigated the efficacy of nanosponge-emulsified phytochemicals in killing M. abscessus biofilms. The nanosponge technology was used to improve the solubility and stability of the phytochemicals, allowing …

A Shift In Rna Fate: Investigating The Role Of C19orf66 During Kshv Lytic Replication, William Rodriguez Jr.

Doctoral Dissertations

During viral infection, virus and host clash for control of the cell in a conflict that ultimately drives the evolution of both sides and has lasting consequences in the form of pathogenesis. At the heart of this struggle is a contest for control of cellular gene expression, a struggle epitomized by an evolutionary tug-of-war for supremacy over RNA fate. During lytic replication, Kaposi’s sarcoma-associated herpesvirus (KSHV) triggers a massive RNA decay event known as viral “Host Shutoff” which decimates greater than 70% of the host transcriptome, simultaneously suppressing the cellular anti-viral response and freeing host resources for viral replication. However, …

Molecular Biodiversity Of Foraminifera, Rabindra Thakur

Masters Theses

Foraminifera are a diverse clade of mostly shell-building single-celled organisms. Estimation of foraminiferal diversity is critical for understanding past and present climatic conditions, as they are highly sensitive to environmental perturbations. Biodiversity estimates of foraminifera began with the counting of test (i.e., shell) microfossils composed of calcium carbonate, as they are well preserved in sediment samples. However, this view has changed with molecular biodiversity estimates, which suggest that early-diverging single-chamber (i.e., "monothalamid") species that lack preservation ability are more diverse than anticipated. Although biodiversity estimates of foraminifera at the molecular level have changed our perceptions, they possess various challenges, especially …

Bifidobacterial Metabolism Of Fucosylated Human Milk Oligosaccharides Influences Structure And Function Of The Infant Gut Microbiome, Liv R. Dedon

Doctoral Dissertations

Human milk contains human milk oligosaccharides (HMOs) that are indigestible and pass intact through the infant gastrointestinal tract where they are available for microbial metabolism. HMOs incorporate the same monosaccharide building blocks but vary structurally in primary sequence of monomeric components. Primary sequences are further diversified by degree of polymerization, branching, and secondary modifications such as fucosylation. Fucosylated HMOs (fHMOs) are highly abundant and can account for over 30% of total HMOs. Infant-colonizing Bifidobacterium longum subsp. infantis (B. infantis) possesses a specialized gene cluster conveying the ability to metabolize fHMOs. This study presents an in-depth analysis of B. …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

The Sos Response In Escherichia Coli K12: An Exploration Of Mutations In Lexa And Reca Using Fluorescence Microscopy, Steven Van Alstine

Doctoral Dissertations

Faithful replication of the genome is paramount for maintaining the fitness of an organism. Therefore, life has evolved inducible mechanisms to be able to repair damaged DNA and maintain evolutionary fitness. The SOS response is a highly conserved DNA damage inducible response that is tightly regulated. Multiple factors contribute to the ability of the cell to perform proper DNA repair and induction of the SOS response including the amount of RecA, mutations in RecA that affect competition for DNA, and other proteins that interact with the RecA filament. The complex relationship between RecA and LexA is the subject of this …

Principles Of Aaa+ Proteases, Samar Mahmoud

Doctoral Dissertations

ATPases associated with diverse cellular activities (AAA+) proteases in bacteria help maintain protein homeostasis by degrading misfolded and regulatory proteins. While a handful of protein targets for these proteases have been identified in Caulobacter crescentus and other organisms, more research is needed to elucidate mechanisms that govern substrate specificity. In the second chapter of this thesis, I will elaborate on how AAA+ substrate specificity is less rigid than previous work has suggested and how limiting ATP or mutations can alter substrate preferences of the ClpXP protease. In the third chapter, I will highlight our efforts to use a quantitative proteomics …

Biomedical Applications Of Protein Films And Polymeric Nanomaterials, Sanjana Gopalakrishnan

Doctoral Dissertations

Biomaterials are widely applied for the diagnosis and treatment of numerous diseases. In addition to fulfilling specific biological functions, biomaterials must also be non-toxic, biocompatible, and sterilizable to be regarded as safe-for-use. Polymers are excellent candidates for fabricating functional biomaterials due to their wide availability and varied properties and may be natural or synthetic. Polymer precursors are fabricated into coatings, foams, scaffolds, gels, composites, and nanomaterials for several biomedical applications. This dissertation focuses on two types of polymeric biomaterials – protein-based materials and synthetic polymeric nanoparticles. Proteins are biopolymers that naturally occur with a variety of structural and functional properties. …

Screening For Binding Partners And Protein-Protein Interactions Of A Fungal Transcription Factor- Xdr1, Nishadi Punsara Gallala Gamage

Masters Theses

Clarireedia spp. (formerly Sclerotinia homoeocarpaF.T. Bennett) is the causal agent dollar spot, the most economically important turfgrass disease impacting golf courses in North America. The most effective strategy for dollar spot control is repeated application of multiple classes of fungicides. However, reliance on chemical application has led to resistance to four classes of fungicides as well as multidrug resistance (MDR). Fungi are known to detoxify xenobiotics, like fungicides, through transcriptional regulation of three detoxification phases: modification, conjugation and secretion. Little is known, however, of the protein-protein interactions that facilitate these pathways. Following next-generation RNA sequencing of Clarireedia spp., a …

Size Progression Of Oxygenic Photogranules (Opgs) And Its Effect On Opg Wastewater Treatment, Ahmed S.A. Abouhend

Doctoral Dissertations

In recent years, the oxygenic photogranule (OPG) process has gained increasing interest because of its potential to treat wastewater without supplemental aeration. Oxygenic photogranules (OPGs) are dense spherical aggregates comprised of phototrophic and nonphototrophic microorganisms. In OPG wastewater treatment reactors, photogranules grow in number as well as in size. The primary goal of this dissertation was to investigate how OPGs grow in size and how the growth affects their structure and functions. We found that OPGs undergo structural changes as they grow bigger in size. As OPGs grow larger, filamentous cyanobacteria become enriched while other phototrophic microbes diminish significantly. OPGs …

Community Assembly And Stress Response Of Grassland Phyllosphere Bacteria, Emily Bechtold

Doctoral Dissertations

Grasslands are an important ecosystem with potential to help stabilize food security and reduce greenhouse gas levels. As global temperatures rise, weather patterns are predicted to drastically change. The resulting increase in intensity, duration, and frequency of drought in important grassland areas will not only affect agricultural production, but also increase grassland susceptibility to fire, disease, and soil erosion. Thus, developing ways to sustainably promote grassland health and production is essential to increase food security and reduce environmental strain. Microbes in the phyllosphere, or aerial surface of plants, promote host fitness through phytohormone and nutrient production, increased stress tolerance, and …

Mapping Selected Polyphenols Metabolism By Gut Bacteria And Their Genes, Ermin Zhao

Doctoral Dissertations

The human gut microbiome is a huge enzyme repository for dietary polyphenols metabolism, especially considering most of the polyphenols cannot be digested in the host and their biological functions are limited. Poor bioaccessibility based on traditional pharmaceutical ADME (absorption, distribution, metabolism, and excretion) assessment is the main problem facing the widely medical application of most polyphenols. Gut bacteria have the potential to mediate a wide range of biotransformation reactions of polyphenols, which leads to the production of many bioactive metabolites. In the past decades, mounting evidence in traditional ADME study have demonstrated gut bacteria play an irreplaceable role in dietary …

Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas

Masters Theses

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has been widely …

The Effect Of Disturbance And Invasion On Fungal And Plant Communities Over An Elevational Gradient, Adam N. Trautwig

Doctoral Dissertations

High-elevation ecosystems are at risk of disruption from the future effects of climate change. Sub-alpine meadows are a source of unique plant populations, intraspecific variation of elevationally extreme populations, and vital sources of fresh water resources. We evaluated the whole fungal communities, arbuscular mycorrhizal fungal (AMF) communities, plant communities, and edaphic variables of sub-alpine meadows in undisturbed, disturbed, and disturbed with a non-native member of the Brassicaceae (Thlaspi arvense) plots. In conjunction with measuring the effects of disturbance on native communities we conducted potting experiments on a dominant grass of sub-alpine meadows (Festuca thurberi). We also …

The Role Of Low-Molecular Weight Fungal Metabolites In Eutypa Dieback Grapevine Trunk Disease, Dana Sebestyen

Masters Theses

Eutypa dieback, one of several grapevine trunk diseases (GTDs), is of serious concern to the grape industry globally. This disease is caused by the fungus Eutypa lata but it is often seen in consortia growth with Phaeoacremonium minimum and Phaeomoniella chlamydospora. It is vital to understand the mechanisms for how this disease functions to develop control measures to combat it. Brown rot fungi are able to use a complex of low molecular weight (LMW) metabolites to induce a Fenton reaction to deconstruct woody tissue. These metabolites are part of a chelator mediated Fenton (CMF) chemistry that produces reactive oxygen …

Structure-Function Studies Of The Trypanosome Mitochondrial Replication Protein Polib, Raveen Armstrong

Masters Theses

Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand …

Extracellular Polymeric Substances In Oxygenic Photogranules: Investigation Of Their Role In Photogranulation In A Hydrostatic Environment, Wenye Camilla Kuo-Dahab

Doctoral Dissertations

The purpose of this dissertation was to assess the critical role of extracellular polymeric substances (EPS) in the photogranulation of activated sludge, in a hydrostatic environment. The first section evaluates the fate and dynamics of different fractions of EPS in sludge-based photogranulation under hydrostatic conditions. The study shows that during the transformation of activated sludge into a photogranular biomass, sludge’s base-extractable proteins selectively degrade. Strong correlations between base-extracted proteins and the growth of chlorophyll a and chlorophyll a/b ratio suggest that the bioavailability of this organic nitrogen is linked with selection and enrichment of filamentous cyanobacteria under hydrostatic conditions. The …

Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos

Masters Theses

Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate …

Physiological Constraints, Mechanisms, And Mineral Transformations Of Iron Reduction In Hyperthermophilic Crenarchaea, Srishti Kashyap

Doctoral Dissertations

Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and typically relies on microbe-mineral interactions that transform various iron oxide minerals. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the mineral transformations that occur due to this metabolism are poorly understood. This dissertation improves our fundamental understanding of the physiological mechanisms and mineral transformations of hyperthermophilic iron reduction using two model crenarchaea, Pyrodictium delaneyi and Pyrobaculum islandicum. Using growth yields and metabolite production rates, we demonstrated that a broad range of Fe(III) (oxyhydr)oxides of variable thermodynamic stability was …

The Shape Of U: Mapping Out Protective Elements In Mrna Escapees, Jacob Miles

Masters Theses

A crucial step of the viral life cycle of Kaposi’s Sarcoma Herpesvirus (KSHV) lytic infection is the triggering of a massive RNA decay event termed “Host Shutoff”. Host Shutoff is driven by the viral endonuclease SOX which leads to the destruction of over 70% of the total transcriptome. This process cripples cellular gene expression and allows for viral reprograming of the cell for the purpose of viral replication. Co-evolution has led to the host developing a multitude of antiviral defenses aimed at preserving certain cellular RNAs linked to antiviral responses. One such defense are RNA secondary structures located within the …

Micro-Physiological Models To Mimic Mucosal Barrier Complexity Of The Human Intestine In Vitro, Abhinav Sharma

Doctoral Dissertations

The mucosal barrier in the intestine is vital to maintain selective absorption of nutrients while protecting internal tissues and maintaining symbiotic relationship with luminal microbiota. This bio-barrier consists of a cellular epithelial barrier and an acellular mucus barrier. Secreted mucus regulates barrier function via in situ biochemical and biophysical interaction with luminal content that continually evolves during digestion and absorption. Increasing evidence suggests that a mucus barrier is indispensable to maintain homeostasis in the gastrointestinal tract. However, the importance of mucus barrier is largely underrated for in vitro mucosal tissue modeling. The major gap is the lack of experimental material …

Dietary Oligosaccharides Modulate Bifidobacterial Production Of The Neurotransmitter Gamma-Aminobutyric Acid, Michelle Rozycki

Masters Theses

Bifidobacteria are the predominant members of the infant gut, colonize adults to a lesser extent, and are recognized as beneficial microbes. Various bifidobacterial species produce ��-aminobutryic acid (GABA), the chief inhibitory neurotransmitter in the mammalian central nervous system. It is postulated that in order to produce GABA, the bifidobacterial genome must contain the gadB and gadC genes which encode a glutamate decarboxylase and a glutamate/GABA antiporter, respectively. Once exported by GadC, GABA is absorbed and transported systemically throughout the host. We hypothesize that specific dietary oligosaccharides will modulate bifidobacterial production of GABA due to varying intracellular concentrations of glutamate. To …

Dissecting Regulatory Mechanisms Of Quorum Sensing Pathways In Bacillus Subtilis, Patrick Hill

Doctoral Dissertations

Living organisms generally share a small number of characteristics, among which include maintaining homeostasis, growth, and responding to changing environments. Wherever we find life, we typically observe this life performing these tasks. Likely no environment is truly barren, so organisms must be able to continue living in crowded conditions. Humans use their senses to determine the quality of their local environment. Individuals use languages, written, spoken and digital to communicate these findings to their neighbors. Bacteria have evolved complex systems to sense these conditions, and to trigger appropriate developmental programs to help them survive, grow, and respond in changing environments. …